Go Analysis From De-Genes

Question

[Phil S.]

Hi there,

I got a set of human gene names with the associated CPM/RPKM/FC/p-Values and want to know if there is an accumulation of some GO Terms in those differentially expressed genes? Any Idea which tool to use? Since it's just a follow-up on a project I did it should not be use 'too much' time to get a result. Ofc, instant solution is also not desireable!

Thanks a lot...

Phil

[ivivek_ngs]

If you have a list of genes that are differentially expressed for your experimental set of conditions then you can check the DAVID website that will help you do the GO analysis for your gene list. Its very simple to you. http://david.abcc.ncifcrf.gov/summary.jsp Check the link and do a functional annotation of your list of genes, for select identifiers , click the drop down to select the official gene symbols if they are and run the analysis.

[Phil S.]

Thank you all guys for your time, I will check out DAVID for sure! (sry for the late response...)

Answer 1

[Biojl]

You can use David, upload your list and run the functional clustering analysis. It will use GO terms but also other sources of information such as domains, localization, protein attributes...

Answer 2

[karl.stamm]

Your fastest solution would be to upload the list to a complete online tool like DAVID. If you have a few minutes I prefer to map gene ids to entrez ids and use bioconductor/GOSeq. If you have a few more minutes, GenMapp-CS can generate enriched pathway diagrams too.

Answer 3

[Floris Brenk]

If you have a lot of minutes you could ask a free trial of IPA Ingenuity http://www.ingenuity.com/products/ipa This program creates beautiful pathways etc etc